The genome sequence of a muscid fly, Polietes domitor (Harris, 1780)

We present a genome assembly from an individual female Polietes domitor (muscid fly; Arthropoda; Insecta; Diptera; Muscidae). The genome sequence is 1,043.3 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 19.95 kilobases in length.

Polietes domitor has a Palaearctic distribution, where it is present in the Azores, from Portugal and the Archipelago of Britain and Ireland through Russia, China to Japan, northwards to northern Scotland, Lapland, and Yakutia (Pont, 1986).In Britain, P. domitor is recognised as a common species, with a flight period mostly from May to September (d'Assis Fonseca, 1968;NBN Atlas Partnership, 2023), yet in continental Europe it is not too common and becomes increasingly rare towards the Mediterranean region (Gregor et al., 2002).Adult insects are associated with animal carrion and faeces, while larvae develop exclusively in the dung of large herbivorous mammals.In the third instar, larvae may become highly predacious, preying on other larvae (Skidmore, 1985), and P. domitor has been considered an important biological control agent of other concomitant muscid species.However, P. domitor larvae are not obligatory carnivores and may reach maturity even without access to a living prey.
The provided genome herein will serve as a source of information for phylogenomic purposes and may be used in comparative genomic studies to answer questions regarding biological adaptations in Polietes and the muscid subfamily Muscinae.
We present a chromosomally complete genome sequence for Polietes domitor, based on one female specimen from Wytham Woods, as part of the Darwin Tree of Life Project.This project is a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland.

Genome sequence report
The genome was sequenced from one female Polietes domitor (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.76,.A total of 27-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 154 missing joins or mis-joins and removed 22 haplotypic duplications, reducing the assembly length by 5.16% and the scaffold number by 20.83%, and increasing the scaffold N50 by 17.93%. The final assembly has a total length of 1,043.3Mb in 778 sequence scaffolds with a scaffold N50 of 190.7 Mb (Table 1).The snailplot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3.The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla.Most (96.07%) of the assembly sequence was assigned to 6 chromosomal-level scaffolds, representing 5 autosomes and the X sex chromosome.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.

Sample acquisition and nucleic acid extraction
The specimen used for DNA sequencing was a female Polietes domitor (specimen ID Ox001318, ToLID idPolDomi1), netted in Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.76, longitude -1.34) on 2021-04-23.The specimen was collected and identified by Steven Falk    II instrument.Hi-C data were also generated from head and thorax tissue of idPolDomi2 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.which runs MitoFinder (Allio et al., 2020) or MITOS (Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.

Genome assembly, curation and evaluation
A Hi-C map for the final assembly was produced using bwa-mem2 (Vasimuddin et al., 2019) in the Cooler file format (Abdennur & Mirny, 2020).To assess the assembly metrics, the k-mer completeness and QV consensus quality values were calculated in Merqury (Rhie et al., 2020).This Table 3 contains a list of relevant software tool versions and sources.

Wellcome Sanger Institute -Legal and Governance
The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner.The submission of materials by a Darwin Tree of Life Partner is subject to the 'Darwin Tree of Life Project Sampling Code of Practice', which can be found in full on the Darwin Tree of Life website here.By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project.
Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature 3. Software tools: versions and sources.

Software tool Version
of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use.
The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible.The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material

Richard P Meisel
University of Houston, Houston, Texas, USA The authors generated a chromosome scale assembly of the female Polietes domitor genome, consisting of six chromosomes.Five of the chromosomes are inferred to be autosomal and one was assigned as the X chromosome, consistent with what would be expected for a calyptrate genome.My only suggestion for a worthwhile addition would be to assign each of the chromosomes to a "Muller element" Brachyceran genomes are organized into six chromosomal units (elements A-F), with element F representing the ancestral X chromosome.The authors have already assigned one chromosome to X=F.They could perform a homology search against Drosophila to assign the remaining chromosomes to their corresponding elements (A-E).This additional analysis would increase the value of this resource.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Evolutionary genetics and genomics I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Figure 2 .
Figure 2. Genome assembly of Polietes domitor, idPolDomi1.1:metrics.The BlobToolKit Snailplot shows N50 metrics and BUSCO gene completeness.The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 1,043,329,465 bp assembly.The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (278,847,389 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (190,665,199 and 149,011,708 bp), respectively.The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude.The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot.A summary of complete, fragmented, duplicated and missing BUSCO genes in the diptera_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Polietes%20domitor/dataset/CANDYM01/snail.

Figure 5 .
Figure 5. Genome assembly of Polietes domitor, idPolDomi1.1:Hi-C contact map of the idPolDomi1.1 assembly, visualised using HiGlass.Chromosomes are shown in order of size from left to right and top to bottom.An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=Omg1UH2-QH26bpDmGk8uPA.
Is the rationale for creating the dataset(s) clearly described?YesAre the protocols appropriate and is the work technically sound?YesAre sufficient details of methods and materials provided to allow replication by others?YesAre the datasets clearly presented in a useable and accessible format?YesCompeting Interests: No competing interests were disclosed.ReviewerExpertise: DNA barcoding, genomics I confirm that I have read this submission and believe that I have an appropriate level of expertise to that it is of an acceptable scientific standard.Reviewer Report 11 April 2024 https://doi.org/10.21956/wellcomeopenres.22852.r77523© 2024 Meisel R.This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
(Oatley et al., 2023) molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up, for which all protocols are available on protocols.io(Dentonetal., 2023b).In sample preparation, the idPolDomi1 sample was weighed and dissected on dry ice(Jay et al., 2023).Tissue from the whole organism was homogenised using a PowerMasher II tissue disruptor(Denton et al., 2023a).HMW DNA was extracted in the WSI Scientific Operations core using the Automated MagAttract v2 protocol(Oatley et al., 2023).The extracted DNA was then sheared into an average fragment size